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<body lang=ZH-CN link=blue vlink=purple style='tab-interval:21.0pt'>

<div class=WordSection1 style='layout-grid:15.6pt'>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>分析模块，输入<span class=GramE>转录组</span></span><span lang=EN-US
style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:
1.0pt'>BAM</span><span style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-font-kerning:1.0pt'>格式的比对结果文件（由分析模块“</span><span lang=EN-US
style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:
1.0pt'>HISAT2</span><span style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-font-kerning:1.0pt'>”生成），以及</span><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>GTF</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>格式的基因注释信息文件，对测序</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>reads</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>在基因组上的比对情况进行统计。统计</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>reads</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>在</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>CDS <span class=SpellE>exon</span>, 5<span
class=GramE>’</span>UTR <span class=SpellE>exon</span>, 3<span class=GramE>’</span>
UTR <span class=SpellE>exon</span>, <span class=SpellE>Intron</span>, <span
class=SpellE>Intergenic</span> regions</span><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>的分布情况。如果基因组上的特征出现重叠（一段区域被两个不同的转录本，同时注释为</span><span
class=SpellE><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>intron</span></span><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>和</span><span
class=SpellE><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>exon</span></span><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>），它们的优先级为：</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>CDS <span class=SpellE>exons</span> &gt; UTR <span
class=SpellE>exons</span> &gt; <span class=SpellE>Introns</span> &gt; <span
class=SpellE>Intergenic</span> regions</span><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>。举例说明，如果一个</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>read</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>比对到</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>CDS <span class=SpellE>exon</span> </span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>和</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'> <span class=SpellE>intron</span></span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>，那么它将被分配到</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>CDS <span class=SpellE>exon</span></span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>。</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><b
style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>输入：</span></b><b
style='mso-bidi-font-weight:normal'><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></b></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>1</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>、</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>bam</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>格式的比对结果文件，由分析模块“</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>HISAT2</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>”生成。</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>2</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>、基因模型文件，即</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>GTF</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>格式的注释信息文件。</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>关于</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>GTF</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>格式的基因注释信息文件，参考链接：（</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>http://asia.ensembl.org/info/website/upload/gff.html</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>）。</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><b
style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>输出：</span></b><b
style='mso-bidi-font-weight:normal'><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></b></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>测序片段比对到基因组上的分布情况。</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>示例：</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>Total Reads<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>40697704<o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>Total Tags<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>57136761<o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>Total Assigned Tags<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>52778989<o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>=====================================================================<o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>Group<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><span class=SpellE>Total_bases</span><span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><span class=SpellE>Tag_count</span><span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>Tags/Kb<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span class=SpellE><span
lang=EN-US style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>CDS_Exons</span></span><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'><span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>40352576<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>43272321<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>1072.36<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>5'UTR_Exons<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>5014479<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>2225814<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>443.88<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>3'UTR_Exons<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>12606669<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>6289491<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>498.90<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span class=SpellE><span
lang=EN-US style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>Introns</span></span><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'><span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>47398527<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>683492<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>14.42<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>TSS_up_1kb<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>59666713<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>50438<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>0.85<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>TSS_up_5kb<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>180276632<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>201632<span style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>1.12<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>TSS_up_10kb<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>232813084<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>217079<span style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>0.93 <span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>TES_down_1kb<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>57134195<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>34368<span style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>0.60<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>TES_down_5kb<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>174704232<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>68430<span style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>0.39<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>TES_down_10kb<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>230273132<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>90792<span style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>0.39<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><o:p></o:p></span></p>

<p class=MsoNormal align=left style='text-align:left;text-indent:20.0pt;
mso-layout-grid-align:none;text-autospace:none'><span lang=EN-US
style='font-size:11.0pt;font-family:宋体;mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:宋体'>=====================================================================<o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>说明如下所示：</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoListParagraph style='margin-left:41.0pt;text-indent:-21.0pt;
mso-char-indent-count:0;mso-list:l0 level1 lfo2'><![if !supportLists]><span
lang=EN-US style='mso-bidi-font-size:12.0pt;font-family:Wingdings;mso-fareast-font-family:
Wingdings;mso-bidi-font-family:Wingdings;mso-font-kerning:1.0pt'><span
style='mso-list:Ignore'>l<span style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><span
class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>“</span></b></span><b
style='mso-bidi-font-weight:normal'><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>Total Reads</span></b><b
style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>“</span></b><b
style='mso-bidi-font-weight:normal'><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>: </span></b><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>This does NOT include those QC <span class=SpellE>fail,duplicate</span>
and non-primary hit reads<o:p></o:p></span></p>

<p class=MsoListParagraph style='margin-left:41.0pt;text-indent:-21.0pt;
mso-char-indent-count:0;mso-list:l0 level1 lfo2'><![if !supportLists]><span
lang=EN-US style='mso-bidi-font-size:12.0pt;font-family:Wingdings;mso-fareast-font-family:
Wingdings;mso-bidi-font-family:Wingdings;mso-font-kerning:1.0pt'><span
style='mso-list:Ignore'>l<span style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><span
class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>“</span></b></span><b
style='mso-bidi-font-weight:normal'><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>Total Tags</span></b><span
class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>“</span></b></span><b
style='mso-bidi-font-weight:normal'><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>: </span></b><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>reads spliced once will be counted as 2 tags, reads
spliced twice will be counted as 3 tags, etc. And because of this, “Total Tags”
&gt;= “Total Reads”<o:p></o:p></span></p>

<p class=MsoListParagraph style='margin-left:41.0pt;text-indent:-21.0pt;
mso-char-indent-count:0;mso-list:l0 level1 lfo2'><![if !supportLists]><span
lang=EN-US style='mso-bidi-font-size:12.0pt;font-family:Wingdings;mso-fareast-font-family:
Wingdings;mso-bidi-font-family:Wingdings;mso-font-kerning:1.0pt'><span
style='mso-list:Ignore'>l<span style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><span
class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>“</span></b></span><b
style='mso-bidi-font-weight:normal'><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>Total Assigned Tags</span></b><b
style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>“</span></b><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>: number of tags that can be unambiguously assigned the
10 groups (see above table).<o:p></o:p></span></p>

<p class=MsoListParagraph style='margin-left:41.0pt;text-indent:-21.0pt;
mso-char-indent-count:0;mso-list:l0 level1 lfo2'><![if !supportLists]><span
lang=EN-US style='mso-bidi-font-size:12.0pt;font-family:Wingdings;mso-fareast-font-family:
Wingdings;mso-bidi-font-family:Wingdings;mso-font-kerning:1.0pt'><span
style='mso-list:Ignore'>l<span style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>Tags assigned to “TSS_up_1kb” were also assigned to
“TSS_up_5kb” and “TSS_up_10kb”, tags assigned to “TSS_up_5kb” were also
assigned to “TSS_up_10kb”. Therefore, “Total Assigned Tags” = <span
class=SpellE>CDS_Exons</span> + 5’UTR_Exons + 3’UTR_Exons + <span class=SpellE>Introns</span>
+ TSS_up_10kb + TES_down_10kb.<o:p></o:p></span></p>

<p class=MsoListParagraph style='margin-left:41.0pt;text-indent:-21.0pt;
mso-char-indent-count:0;mso-list:l0 level1 lfo2'><![if !supportLists]><span
lang=EN-US style='mso-bidi-font-size:12.0pt;font-family:Wingdings;mso-fareast-font-family:
Wingdings;mso-bidi-font-family:Wingdings;mso-font-kerning:1.0pt'><span
style='mso-list:Ignore'>l<span style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>When assign tags to genome features, each tag is
represented by its middle point.<o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
class=SpellE><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>RSeQC</span></span><span lang=EN-US
style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:
1.0pt'> cannot assign those reads that:<o:p></o:p></span></p>

<p class=MsoListParagraph style='margin-left:41.0pt;text-indent:-21.0pt;
mso-char-indent-count:0;mso-list:l1 level1 lfo4'><![if !supportLists]><span
lang=EN-US style='mso-bidi-font-size:12.0pt;font-family:Wingdings;mso-fareast-font-family:
Wingdings;mso-bidi-font-family:Wingdings;mso-font-kerning:1.0pt'><span
style='mso-list:Ignore'>l<span style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><span
class=GramE><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>hit</span></span><span lang=EN-US
style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:
1.0pt'> to <span class=SpellE>intergenic</span> regions that beyond region
starting from TSS upstream 10Kb to TES downstream 10Kb.<o:p></o:p></span></p>

<p class=MsoListParagraph style='margin-left:41.0pt;text-indent:-21.0pt;
mso-char-indent-count:0;mso-list:l1 level1 lfo4'><![if !supportLists]><span
lang=EN-US style='mso-bidi-font-size:12.0pt;font-family:Wingdings;mso-fareast-font-family:
Wingdings;mso-bidi-font-family:Wingdings;mso-font-kerning:1.0pt'><span
style='mso-list:Ignore'>l<span style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><span
class=GramE><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>hit</span></span><span lang=EN-US
style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:
1.0pt'> to regions covered by both 5’UTR and 3’ UTR. This is possible when two
head-to-tail transcripts are overlapped in UTR regions.<o:p></o:p></span></p>

<p class=MsoListParagraph style='margin-left:41.0pt;text-indent:-21.0pt;
mso-char-indent-count:0;mso-list:l1 level1 lfo4'><![if !supportLists]><span
lang=EN-US style='mso-bidi-font-size:12.0pt;font-family:Wingdings;mso-fareast-font-family:
Wingdings;mso-bidi-font-family:Wingdings;mso-font-kerning:1.0pt'><span
style='mso-list:Ignore'>l<span style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><span
class=GramE><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>hit</span></span><span lang=EN-US
style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:
1.0pt'> to regions covered by both TSS upstream 10Kb and TES downstream 10Kb.<o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>分析模块引用了</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>RSeQC-2.5</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>软件包（</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>http://rseqc.sourceforge.net/</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>）。</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>相关文献如下所示：</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>Wang, L., Wang, S., &amp; Li, W. (2012). <span
class=SpellE>RSeQC</span>: quality control of RNA-<span class=SpellE>seq</span>
experiments. Bioinformatics (Oxford, England), 28(16), 2184�C2185.
http://doi.org/10.1093/bioinformatics/bts356<o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>Wang, L., <span class=SpellE>Nie</span>, J., <span
class=SpellE>Sicotte</span>, H., Li, Y., <span class=SpellE>Eckel-Passow</span>,
J. E., <span class=SpellE>Dasari</span>, S., et al. (2016). <span class=GramE>Measure
transcript integrity using RNA-<span class=SpellE>seq</span> data.</span> BMC
Bioinformatics, 17(1), 1�C16. http://doi.org/10.1186/s12859-016-0922-z<o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

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